A high-continuity and annotated tomato reference genome

Abstract

Background Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. Results Here, we assembled an updated reference genome of S. lycopersicum cv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato. Conclusion Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.

RepeatOBserver: tandem repeat visualization and centromere detection

“…Chromosomes are the black dots, Shannon diversity is plotted in red and the histograms are plotted in light blue. Species included are: Mouse-ear cress - A. thaliana (COLCEN assembly) (Naish et al, 2021), Human - Homo sapiens, Fruit fly - Drosophila pseudoobscura lowei (Bracewell et al ., 2019), Rice - Oryza sativa (Japonica Group) (Nawaz et al ., 2014), Turnip - Brassica rapa (Zhang et al ., 2023), Strawberry - Fragaria vesca (Zhou et al ., 2023), Sunflower - H. annuus (HA412) (Huang et al, 2022), Tomato - Solanum lycopersicum (Su et al ., 2021), Chicken - Gallus gallus domesticus (Piégu et al ., 2018), Mouse - Mus musculus (Hughes et al ., 2007), and Maize - Zea mays (Jiao et al ., 2017).…”

“…Although centromeres are both genetically and epigenetically determined, we find that natural centromere positions in most of the chromosomes that we explored could be determined based on the repetitiveness of the underlying genetic sequence without the need for epigenetic information. (Naish et al, 2021), Human -Homo sapiens, Fruit fly -Drosophila pseudoobscura lowei (Bracewell et al, 2019), Rice -Oryza sativa (Japonica Group) (Nawaz et al, 2014), Turnip -Brassica rapa (Zhang et al, 2023), Strawberry -Fragaria vesca (Zhou et al, 2023), Sunflower -H. annuus (HA412) (Huang et al, 2022), Tomato -Solanum lycopersicum (Su et al, 2021), Chicken -Gallus gallus domesticus (Piégu et al, 2018), Mouse -Mus musculus (Hughes et al, 2007), and Maize -Zea mays (Jiao et al, 2017).…”

Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato

“…Moneyberg [93] , S. lycopersicum cv. Heinz 1706 [94] , and S. lycopersicoides acc. LA2951 [95] ( Table 2 ).…”

Long-read sequencing of extrachromosomal circular DNA and genome assembly of aSolanum lycopersicumbreeding line revealed active LTR retrotransposons originating fromS. peruvianumL. introgressions

“…Transposable elements are ubiquitous components of plant genomes. LTR retrotransposons (LTR-RTEs) are among the highest copy members of the plant mobilome (Feschotte, Jiang, & Wessler, 2002; Zemach et al, 2013), accounting for 76% of the rye genome (G. Li et al, 2021) and 50% of the tomato genome (Su et al, 2021). Uncontrolled TE reactivation can lead to genetic instability.…”